Hi I do not know which services you are using. But i can explain to you that as far as I have seen ISPConfig changes httpd.conf.

When it changes it does make a backup copy of httpd.conf renaming it to httpd.conf.orig, it also creates an exact copy of the changed file but with a different name httpd.conf appending at the end of the name the date and time of when that change was made.

It also changes /etc/postfix/main.cf

It does include the following orders
virtual_maps = hash:/etc/mail/virtusertable

mydestination = /etc/mail/local-host-names

In my case it commented this one.
virtual_alias_maps = hash:/etc/postfix/virtual
which was fed by virtualmin where all my email address names are stored.

/home/my_IP_number folder was created and access logs can be found there.
/home/admispconfig folder was created inside various files and mail stats folder
/home/web1 folder
/home/web2 folder
also created